Refugees crossed back to their home country and will be given humanitarian needs before they return to their respective homes, said Felix Niyiragira, head of Ngozi province in Burundi.
The official admitted that the refugees had fled their country due to insecurity and hunger.
"Government has assured the returnees total security and we feel there is a step taken since the last referendum elections," Niyigira said, adding that precautions have been taken to beef up security as the general elections draw closer in Burundi.
Nearly 5,000 Burundi refugees still remain in Rwanda, he said. "We are using all possible means to get them back and what I can say is, we are half way done."
Both governments of Rwanda and Burundi came to a common consensus in May of sending back the refugees, a decision that frightened most international human rights bodies.
Thousands of Rwandan refugees also fled to Burundi and Uganda in April and May citing fears of their lives in the ongoing traditional courts of Gacaca that tries genocide suspects.